SMTL ID : 9god.1 (1 other biounit)

Crystal structure of DPP9 in complex with N-phosphono-(S)-3-aminopiperidine-2-one-based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 x 01: ethoxy-[2-(4-pentylphenyl)sulfanylethyl]phosphinous acid

01.1: 12 residues within 4Å: Chain A: E.230, E.231, Y.626, Q.630, S.712, Y.713, V.738, Y.744, Y.748, N.792, V.793, H.822 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.630, A:V.738, A:Y.744, A:Y.748 Hydrogen bonds: A:Y.713 Water bridges: A:Y.744 01.12: 15 residues within 4Å: Chain B: E.230, E.231, F.232, D.233, H.482, Y.626, Q.630, S.712, Y.713, V.738, W.741, Y.744, Y.748, N.792, H.822 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.233, B:V.738, B:W.741, B:Y.744, B:Y.748 Hydrogen bonds: B:Y.626, B:Y.713

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: F.624, K.642, Y.643 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.642, A:K.642 Water bridges: A:R.645, A:W.711 EDO.3: 5 residues within 4Å: Chain A: K.219, E.261, D.263, K.296, A.298 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: R.289, M.742 Chain B: E.278 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: N.294, P.295, K.296, I.297, V.331, E.332 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.297, A:I.297 Water bridges: A:E.332, A:E.332 EDO.6: 6 residues within 4Å: Chain A: K.330, F.350, L.351, D.352, W.357, Q.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.350 Water bridges: A:K.330 EDO.7: 5 residues within 4Å: Chain A: D.407, I.408, F.409, K.485, I.486 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.409, A:I.486 EDO.8: 7 residues within 4Å: Chain A: E.475, W.476, T.500, K.501, D.502, T.503, P.504 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.501 Water bridges: A:T.500, A:Q.666, A:R.667, A:R.667 EDO.9: 4 residues within 4Å: Chain A: L.505, H.594, Y.604 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.594 EDO.10: 3 residues within 4Å: Chain A: D.502, T.503 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.503, A:T.503 EDO.13: 2 residues within 4Å: Chain B: K.642, Y.643 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.642 EDO.14: 7 residues within 4Å: Chain B: K.330, F.350, L.351, D.352, W.357, L.358, Q.359 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.352, B:W.357 EDO.15: 8 residues within 4Å: Chain B: M.606, Y.608, L.633, V.634, K.639, Y.643, L.646, V.658 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.608, B:L.633

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 1 residues within 4Å: Chain A: F.412 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sewald, L. et al., Sulphostin-inspired N-phosphonopiperidones as selective covalent DPP8 and DPP9 inhibitors. Nat Commun (2025)

Release Date

2025-07-16

Peptides

Dipeptidyl peptidase 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Dipeptidyl peptidase 9

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